6-71647057-T-C

Variant names:

• chr6-71647057-T-C
• rs9446432

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.134 in 152,084 control chromosomes in the GnomAD database, including 1,763 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1763 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20386 AN: 151968 Hom.: 1750 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.0502

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0745

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.125

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.134 AC: 20441 AN: 152084 Hom.: 1763 Cov.: 33 AF XY: 0.134 AC XY: 9995 AN XY: 74334

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.0502

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.0740

Gnomad4 FIN AF: 0.0698

Gnomad4 NFE AF: 0.0845

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0908 Hom.: 348

Bravo AF: 0.153

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9446432; hg19: chr6-72356760;